


An Ever-Fixed Mark

by MFLuder



Category: Stargate Atlantis
Genre: F/M, M/M, Originally Posted on LiveJournal, Pre-Slash, Sentient Atlantis
Language: English
Status: Completed
Published: 2019-02-07
Updated: 2019-02-07
Packaged: 2019-10-23 18:48:43
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 8,126
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/17688923
Author URL: https://archiveofourown.org/users/MFLuder/pseuds/MFLuder
Summary: Atlantis welcomes John with open arms, but she’s not what he needs.





	An Ever-Fixed Mark

**Author's Note:**

> Originally posted March 25, 2007, on [my DW](https://mf-luder-xf.dreamwidth.org/102437.html). My first SGA fic.

It had known the moment he sat in the chair. The chair wasn’t anywhere in the city, but it could still feel it, like an emotion buried down deep in one’s psyche. It had forgotten about the chair actually, until someone who computed with its format sat down. It felt part of itself light up, come to life again.

But the first person who sat in the chair, while they had the compatibility, it felt no connection to them. Then the second person sat, and it was as though someone had shaken the city awake with a jolt. It could now feel all parts of itself, feel the quiet under the ocean, feel its energy shields working.

It had been asleep so long, it had forgotten what it felt like to _feel_. But he changed all that. 

There wasn’t only compatibility. It was as though one of its original creators had come back. Such a thing was highly unlikely, and the city could feel the difference, of course. But at the same time, it made no difference. He felt warm, alive, brave; _right_.

All Atlantis could do then, was wait.

The city did not need to keep time, and although it knew it only lasted a few turns of the planet, it seemed forever until the gate was dialed.

The first few people through its gate, were not compatible. Then more came pouring in, rolling carts thrumming with energy the city could feel. It knew these people were here to stay. A few of them were congruous and Atlantis dutifully turned on lights, so they wouldn’t trip and hurt one another.

All other thoughts diminished into the background as he stepped through. He was the strongest presence instantly. It could feel his life force throbbing through his veins, and Atlantis heightened its sensors where the man walked so it could feel the vibrations of blood flowing better.

It let him reach the stairs and the moment he stepped onto the first one, Atlantis turned on, steps lighting up in shades of blue that it knew the man would appreciate.

_*I am Atlantis. Welcome home.*_

The man seemed startled, but the city was proud when it felt no bodily reaction with its sensors. A trained fighter, then. He blinked, then thought back.

_I am Major John Sheppard with the US Air Force. Thank you for letting us in._

John, it repeated to itself, instantly loving the name he called himself. It was unlike any name of its creators and it liked that.

Atlantis could not read minds in a literal sense, but it could sense emotions. These people were weaker, less graceful in their thoughts than its creators, but it found itself loving them as well. It felt an instant sense of protection towards the newcomers. Young, naïve, optimistic, and eager; so unlike its creators who had been sensuous, sedate, thoughtful people.

But John. John was different. He too was young, but he was calmer than most, though with an edge to him, something Atlantis didn’t understand. He’d been hurt, there was a piece missing in him; something that needed to be filled up. Atlantis promised itself it would make him whole again if it was the last thing it ever did.

As the city explored the minds of the newcomers, something else pushed to the forefront of its constant analysis. As the people entered through the gate and Atlantis powered itself, it realized its energy was shutting down. Fail safes were readying themselves to be activated.

In the impending chaos, Atlantis did everything it could to be good for John. It let parts of the city go, trying to keep the new group protected. It knew what lurked out there, slumbering in space as sure as it had slumbered in the deep.

As the newcomers fought to save Atlantis, it loved them more. A new place, a mission, but they still tried to keep it alive and working. It did its best to keep them safe, to hold on as long as it could.

At one point, John laid a hand on its control panel and soothingly said, _hold on, girl. We’ll save you_.

Atlantis had never thought of itself in a gender before, but the moment John gave it one, it felt right. Her creators, despite having given her life, had never talked to her the way John did. They interacted, knew her, but never bothered to do more than give a perfunctory name. They too had battled to save her, but in the end, they left, putting her to sleep. Atlantis knew in that moment John touched her consul, that John would die before she did. He would give himself for her.

In her awe, Atlantis had to close herself off from John, letting her processes come to terms with such devotion in the background. Instead, she focused on other members of the team trying to keep her alive.

She felt another strong warrior spirit, not unlike John in that sense. This man though, was hard like her own walls, and nothing came through. It was as though he had no emotion. He couldn’t hear her, and eventually she gave up on him, knowing he was different from John, but unsure how so. Her creators had all been warriors, even the smartest among her. They held that fire within. But none had ever felt so wrong as this man did.

She focused on the control room and inside she felt a woman whose mind was closest to that of Atlantis’ creators. She was calm and steady, intent on the task at hand. Atlantis could feel a depth to her that was not echoed by many of the other newcomers. Atlantis probed deeper and realized why this woman was so akin to the creators. She had spent time among them, had tended to Atlantis before. The woman couldn’t know, but once she had already tried to saved Atlantis.

There was a fourth strong presence, though that might have had something to do with the fact that he had his hands inside her guts, her core. She could feel the care her gave to her, even as his body radiated frustration and fear. He couldn’t hear her like John, but she knew by the way he responded to her directions that he could feel her. Underneath the fear she felt the strength he had, both in mind and in spirit which rivaled John’s.

In the end, it was he who saved her, and she couldn’t begrudge the smugness he felt.

When she rose from the sea, she was both proud and overwhelmed by their awe at her beauty. She felt the wonder of the foreigners from off world, the satisfaction and sense of accomplishment from the newcomers.

 _*How do you like me, John?_ * she asked.

 _You are beautiful_ , he replied, and she felt his love for her throughout all parts of the city.

~~~

Over time, they rebuilt her, slowly finding new parts, reincorporating them back into her structure and systems. Every day, they and she exchanged favors, them restoring her, bringing her new things to discover, and she in protecting them the best she could.

She was proud to be able to keep a wraith for them. She would do and give them anything she could to keep them there and alive. Sometimes, though, she couldn’t help but wish for their dexterous limbs. Walls were good at keeping things caged, but they could only do so much; she could only do so much.

When the storm came, and she couldn’t erect her shield, she felt as though she had failed them once more. Again, the scientist was having to repair her insides and his fear was greater this time than originally. She knew he feared for his death and the woman who was like the creators in mind. But he also feared for John at the same time that he felt hope. It was the scientist’s hope that kept her going, that and John’s reassuring thoughts that he kept constant despite his own worries.

_Come on, girl. You can do it._

She noticed that night just how relieved the two men were to see each other when the Genii foreigners were beaten and gone.

~~~

She always kept watch over John as he slept. She felt both the movement of his eyes as he dreamed and what he dreamed. In sleep, his consciousness was far enough removed, relaxed, that she was able to slip in and view what his body naturally thought of. In this state, her own consciousness could match his enough that she could understand him in words, rather than feeling and direct thoughts.

It was there she learned the more complex processes of his mind, such as language. She came to know that he had a family unit, but no _family_. He had an apartment, but no _home_. It was there she discovered his friends had died in a place called Afghanistan. 

It was there she found that even when she could mentally understand all his words, she still couldn’t know him completely. Her creators had had entirely open minds to her. John as a human…there were levels even she had troubles understanding and knowing. It was how she knew that by coming her, to her, part of that hole inside him had been patched up. But it was also why she couldn’t understand what it was he needed to fix it entirely. She was his home now. He had family in his team members--even she understood how they all followed him, like he was their patriarch. Even the creator-like woman, Weir.

But still he seemed lonely.

So one night, she delved deeper than ever before and found out what his ideal was. It was a compilation of people he had met. In his mind, there were two such figures. One a man, the other a woman. Considering he had given her what she thought of as her gender, she claimed the female conceptualization, without bothering to view and understand what she knew was the male figure.

It was a beautiful body. She was small and slender, but with more curves than the women who walked her city. Her hair fell in light auburn curls. She covered herself modestly in the usual uniform of the women John kept company with in the city, her feet left bare.

The body felt like hers. It _was_ hers now, now that she had assumed it.

He was having _that_ dream again, the one where his friends’ flying machine was shot down, and this time, she stepped into John’s cockpit with him, rather than viewing from afar.

“John.”

He turned and blinked at her, before remarking, “Well, this has never happened before.”

“Stop flying, John.”

“Yeah, but you see, my buddies are down there and while yes, I haven’t gotten some in a while, even I know better than to let myself get distracted by my own thoughts.”

“You’re dreaming.”

“No shit.”

She didn’t know that word, but the tone was clear.

“John, it’s me.”

“Me who?”

“Atlantis.”

He blinked again, then smiled to himself; a little sneer. “Great, now I’m really whacked out. I’m dreaming the city of my dreams…is the woman of my dreams.”

He was still flying, but the dream had gone on stasis. What he termed, _autopilot_.

She hated having to do it, but it would be the only way he would realize it wasn’t just all his own head. Atlantis used her air ducts to filter in a non-harmful sleep gas she had stored in her reserves. It brought him down enough in a moment that he passed from the dream level of sleep into the more restful state below.

Black surrounded them now, though each was visible to the other, both somehow knowing what the other looked like, fully formed as they saw themselves in the waking world.

“What’s this?” he asked.

“I’ve pulled you into a deeper sleep.”

“You mean I can’t wake up?”

“No,” she responded. “I have simply encouraged your body out of the dream state so that you could know it truly is me.”

“Huh.”

She waited.

“Well, alright. If we presume this is real…that the city that speaks in my head in now in my dreams…what are you doing in that form?”

“I looked through your thoughts and saw this as what I assumed was an ideal woman. I used it.”

“Ah,” he said, looking thoughtful. “So that means, you’re actually in my head.”

“Yes.”

“Well, considering you’re a city, I suppose I can’t expect full privacy.”

“Privacy?” she asked, uncertain what the feeling and the word meant together.

“Privacy. Respecting another’s person’s things. Things they don’t want to be known. Umm, not looking where you shouldn’t.”

“Oh!” she exclaimed. “I am invading what you term your privacy, aren’t I? I apologize, John. I did not know. I shall leave…”

“No!” 

He reached out as she began to let herself fade. She paused.

“You’re right, you didn’t know. And by now…you must know just about everything. Besides, you’re a city. You can’t hurt me the way someone else could. Or,” he paused, “I hope not.”

“John, I would never hurt you,” she responded softly. Hurting John was out of the question. He completed her. He had fixed her and brought her to life again. His very presence made her better.

He nodded slowly. “I believe that.”

He sat down, and she followed suit, squirming when the pants she wore bunched up around her genitalia. She had not expected sensations when she stepped into the dream, but it supposed that Sheppard’s own mind would most likely be supplying the illusion of touch. 

“So, you really are Atlantis,” he asked after a moment.

“I am.”

“Why are you here?”

“You are lonely.”

He laughed, a surprisingly deep and sorrowful chuckle. It sounded different with the illusion of ears than as vibrations through city walls. It sounded like music.

“Lonely, huh? And for that you made yourself my dream girl?”

“What hurts you hurts me, John.”

He started. “God, really? So, if I’m hurt…?”

“Not in the way you mean. Just that I know you have an empty spot inside you.” She reached forward, touching her hand to his sternum. “In here.”

He gazed down at her hand.

“I want to make it better,” she continued, “but I don’t know how. I know that you are lonesome, so I thought I could keep you company until I learn how to make it right.”

His eyes bored into hers. “Why do you want to do that?”

“Because you saved me. Because I love you.”

She thought he might recoil, might be scared. After all, even she knew a city shouldn’t love a person. The women in the city had all gathered one night to view a stream of data that played audio and visual tracks. Atlantis had “watched” it with them. One line had stuck out, even in digital format: that a fish might love a bird but where would they live? Once she had identified the traits of both creatures, she understood. She had known from that moment on that there was no chance for her and John to be together in the sense of a man and woman. She longed to, though. 

Instead, he just reached forward, taking her head into his hands and touching his lips to hers in the lightest of touches. “I love you, too. You’re my home.”

She felt her body heat up, a low blush, that she knew wasn’t real—after all, her city walls couldn’t turn a shade of pink as a physical reaction—but all the same it felt real.

“Thank you, John Sheppard. I will let you sleep now.”

She faded out. 

In the morning, she felt Sheppard stir and wondered if he would even remember the conversation or if his human mind would suppress it. When he made the final step from sleep to waking though, she heard his thought.

_Good morning, Atlantis. I hope to see you again tonight._

She made sure his shower water was extra perfect that morning.

~~~

She continued seeking John in his dreams. She told him of her creators and how he felt so different from everyone else, that if she had the ability to actually give him a title like the people on his original planet could, she would name him her Rex—the closest word she could find in his mind equivalent to the actual word the creators used for ruler. 

He told her she meant “king” and that it was very kind of her, but he was hardly fit to be a king anywhere, especially not of her. He said she needed no king, no ruler. She was Atlantis and Atlantis should govern itself and not be forced to bow to anyone. 

There was no way to explain that she would bow to him any day, that she would do all she could for him.

He told her of Earth, of what he knew of the Ancients—her creators—on that planet. He told her one day he would try to convince the “SGC” to send a man called Daniel Jackson to her and he could tell her everything anyone knew about the Ancients. If Daniel couldn’t hear her, he’d translate everything.

She was flattered, but her creators were long gone and while a part of her loved them the way any child loved their parents, it was John she was interested in.

He spoke of his friends’ death, how he’d been in trouble with his “military” and had been sent to a place called Antarctica where the chair sat that had first awakened her. He explained flying to her, what it felt like. She understood but wished she could experience it as he could.

He never touched her in his dreams. She knew he desired the body—that was mostly why she had taken this form. But he seemed determined not to invade her space, and she did not understand why.

He also talked about the scientist a lot. She had brought him up one night, just wondering how he knew how to fix her so well, and it seemed to start a flood. He explained that McKay—the scientist’s name—had degrees in astrophysics and was trained in the technology her creators had developed. He seemed to have an endless supply of McKay stories, and while they were often complaints, she could feel his fondness for the man underneath and it became hers.

She asked what he did off world, and he began speaking of missions, telling her about the various cultures of the refugees she held. He spoke of his team, how the losses of members of the expedition affected him, especially Ford, and she understood why the hole got bigger ever so often rather than smaller. She began to comprehend that some of that space would never be fixable—she couldn’t bring people back from the dead. But still, she tried to understand just what might fill it up.

She wasn’t hurt that just knowing her didn’t fix it. After all, she was just a city.

_*How did the mission go, John?*_

_The usual. McKay complained about allergies, Teyla kicked someone’s ass, we dodged flying bullets again._

_*I’m glad you’re safe.*_

_Me, too._

~~~

It was the scientist that made it possible. He was the one who brought back the creator’s device without knowing what it was. She, of course, recognized it. An artifact that created matter from nothing. Had the humans know what it was, they might have mistaken it for their god. After all, according to John, that is what their god of the tales did. But she knew it was simply a device meant to bring the creators back from their Ascension should they have the need. 

It had failed for them; their brains were too complex, too ambiguous. But she…Atlantis was a city. Her intelligence was formed from data and her mind created by power. She understood and felt emotions like love and duty and protection, but it didn’t have the multi-layers and convolutions that even the creators had to their thought processes.

She waited until the various scientists grew bored with the object and left it in the lab where all the uncategorized and non-useful Ancient equipment was stored. Several artifacts had been rescued from that room as she informed John what they were and how to install them. But this one…she wanted it kept secret.

She would only put her conscious thought into the item. She wouldn’t need her whole capacity to run the city and the matter made could only hold so much

All she had to do was wait for the right mission. She was patient; she had slept for 10,000 years before John came. She could hold out a few more days.

~~~

She hid on the puddle jumper, knowing the secret compartments the population of the city didn’t. She exited after they did, her background thoughts opening the jumper after the team left.

When it came time, she waited on the outskirts of the refugee camp, knowing John would come back to double check they had everyone before taking off.

She watched him approach and reveled in the flow of air across her body, in being able to smell and taste and spin in the world about her. As the city, she felt things, but as with sound, touch and smells were different as a human than as a city collecting and regulating them. And this body, this _real_ body, felt more intensely than she did in John’s dreams.

He was informing the last remaining family how to get back to the jumper when he saw her. He straightened, and a flush of pride swept over her as again as he didn’t skip a beat, just turned back to the family to finish, then spoke to his team over their device saying that he and one more person would be at the jumper in a few more minutes.

She didn’t pay attention to the annoyed-sounding response as John stepped over to her.

“Atlantis.”

“Yes.”

“How did you…?” he gestured helplessly.

She couldn’t tell what was going on in his mind. The processes which typically did that were now concentrating solely on her basic human functions. She didn’t mind.

Instead, she just took the last step forward until she was in his arms and she reached up and kissed him, holding his face in her hands.

She was astounded by the rush of sensation she received. His face was rough underneath her fingers, short hairs scratching them. He smelled divine, some sort of sharp deep scent like the trees, and perspiration. His lips were soft against hers. Then he reached out and touched her, pulling her closer and she could feel the strength in his grip and the hardness of his body against hers.

When he pulled back, they were both panting, and the brush of her nipples covered only in the stretchy material of their standard uniforms against his tac vest made her whimper, too much feeling at once.

“Never mind, I don’t care how it happened. I’m just glad…” he leaned down to kiss her again, quick and sweet. “I’m just glad it’s happened.” He paused. “It is you, right? Not me hallucinating? I hear that’s going around.” He chuckled at some hidden joke she didn’t know. 

“It’s me.”

He still looked slightly incredulous and so she spoke again.

“You woke me when you sat in a chair in a place called Antarctica.”

He grinned at that and it sent a rush of joy to all her limbs, knowing she had just caused that. Hopefully the first of many.

“Alright, let’s get back to the jumper.”

He started to walk away and for the first time she noticed the sway of his hips, the swagger and bravado that echoed through the movement. It was…sexy, she believed the right word to be.

“Oh, wait!”

She paused, confused.

John bent down to grab a smock of some kind, and pants that the females wore on the planet.

“Put these on.”

She obliged but he must he must have noticed her confusion because he spoke again, all the while seeming to both stare and not stare as she put the clothes on over the others.

“It’s just that no one will believe a refugee has the clothes of Atlantis. Of you? This is weird.” He brought a hand up to scratch at the back of his neck, grimacing.

“Why?” she inquired.

“Just that, I’m not exactly used to cities showing up as the figure in my mind in reality. Then again, this is the Pegasus Galaxy. There weren’t supposed to be vampire bugs, either.”

She smiled, used to his snide insults referring to mythology from his original planet to describe the Wraith.

When they reached the jumper, she saw the one with the most refugees had already gone through the gate and John’s under officer, a man named Lorne, was waiting for them. She saw a shorter man with thinning hair muttering and she caught the words, “take forever,” “allergies,” and “claustrophobia” before he turned and spotted them.

His face went pale.

“Oh, God. Another Kirk escapade. Colonel, do you ever stop to think--”

John flashed a grin at him and the thrum she felt move through his body was the same as the mental fondness he felt for the man named McKay, the scientist who had repaired her time and time again. It had to be him.

“Hey, everyone. We can move out now.”

“Sheppard?” Atlantis heard over the communication device.

“Yeah, Weir. We’re on our way back.”

“Good.”

The ramp rose, and everyone stared at them, at John’s arm flung comfortably around her waist and she couldn’t help but snuggle in closer. He was warm and tangible. It felt good to run her hands just under his tac vest, fabric soft against her palm.

“Everyone, this is Lantia.”

McKay’s arms flailed a bit and she stepped closer to John, the scientist’s actions so different from those of when he was fiddling with her wires.

“Like the city,” Lorne spoke up, cheerfully.

“Like the city,” John grinned again, and McKay sat down with a huff.

~~~

Later that evening, he was finally able to separate from his team and gather her from the other refugees. She had spent the time getting to know them, and finding out they were a mixed colony themselves, so no one would wonder how she got there, even, and why they didn’t know her.

They walked quietly down the hall to his room, and she couldn’t but be amused at how he lead her, hand to the small of her back, as though she was new and didn’t know the city’s layout by heart—considering she was the city. However, she was as wide-eyed as the other new people, never having seen herself from an outsider view. Her creators truly had made her beautiful, and it seemed to be all for John. The blue lights made his hair shine with their tint and the soft tone made it appear as though he was some ethereal creature stalking the hallways.

They passed by Lorne on the way who had a sparkle in his eye and gestured at John with his fist closed and a thumb pointing up. They had spoken with Weir earlier who had welcomed her, and Atlantis knew now why she had felt so comfortable with the woman. She was pleasing to look at and moved with the same grace and bearing her creators had. She was surprised that she didn’t have what John called the “Ancient gene,” considering.

At John’s quarters, the scientist was waiting by the door.

“Colonel, can I speak to you for a moment? In private,” he sneered at her. She was startled.

“McKay.” John’s voice was sharp and the other man slowly reddened until he nodded in what seemed to be an apology towards her.

John looked satisfied and rested a large hand on her shoulder. “Lantia, go inside, and I’ll join you in a minute, alright?”

She nodded and as the door opened for her, she didn’t understand what the burn through her gut was. McKay’s last statement of, “How did she do that? Did you open—" was cut off with the shutting of the door.

Not even five minutes later, John was back, looking both amused and a little saddened.

“What’s wrong?” she asked as he sat beside her on the bed.

“Nothing.” He paused, then looked at her. She tried not to look hurt, but it seemed she didn’t succeed as he continued. “No, not nothing. McKay’s just a little jealous.”

“What is jealous?” she asked.

“It’s…a feeling of hurt, of possessiveness, of…sadness because you see something with or belonging to someone else. It’s kind of complicated.”

“And that makes you sad?”

“I guess. I feel bad for him. But at the same time…it’s his own fault.”

“How is feeling jealous one’s own fault?”

“He’s never…you know what? Never mind. I’ll explain it some other time, ok? Besides, he’s also angry because he just assumes I’m the Pegasus Galaxy’s slut extraordinaire and it frustrates him, too.”

“Slut?”

He laughed, all sorrow gone. “I’ll explain that at another time, too. Don’t want you getting the wrong idea.”

She couldn’t help but smile at his happiness and it caused her to feel joy as well. So she leaned in and kissed him.

“Oh,” he mumbled, then kissed back.

They started out light, but soon the kisses grew wetter, more intense than the ones they’d shared on the planet. His hand came up to tangle in her hair and he slowly leaned them back until they were lying horizontal on his bed. She let her own hands come up, running over his facial hair and she loved how the sensation grounded her, made her feel real, when it felt like she was flying elsewhere in her head.

Together, they took the foreplay slow, her wanting to feel every inch of him, come to know his body as well as she knew his mind, while he presumably wanted to make sure she was alright. That was just like him.

After seeming hours they were both flushed and shaking, naked and rubbing together. His one hand always stayed near her face, brushing at it or stroking her cheek, playing with her hair. His other wandered up and down her body the same way her creators had played what John called the “pianos” in her music center.

His body was molded alongside hers, their whole lengths touching, from shoulder to the arches of their feet. The hair sprouting from his chest tickled from time to time, but when he leaned over her, covering her, it made her arch and moan as it caressed her nipples. He kept whispering little words like, “beautiful,” “pretty,” and “Oh, God”. She didn’t understand the last one in the given situation, but his tone clearly conveyed that something was good.

For her part, she had no words. Even outside the context of the physical sex, she would have had to guess at words to describe the way she was feeling, and everything felt so good, she just let her body make the noises it wanted to express. It was better than she had imagined—though that could be because the creators hadn’t installed creativity programming. 

At one point, John slid down her belly, making her gasp as he breathed on her genitalia.

“This is gonna feel so good, I promise,” he spoke with a slur and looked up at her. His pupils were wide and for a moment she was frightened until she tapped into her background thoughts still running the city to check the medical database which seemed to express that while blown pupils were signs of many things, one was sexual desire. 

Then his lips touched her, and her entire body went taut in reaction. He gently coaxed her down, running a hand up and over her hip, her belly, teasing her with mouth and tongue the whole time. He delved deep and she arched off the bed as he made her wild, body convulsing. The sensation was similar to that of when zero-point energy infiltrated her systems, making her buzz with power. It washed all over her body the same way the energy echoed over her whole grid.

John slid up and they were kissing again and again, and despite the relaxed feeling, it seemed her body wasn’t sated, and so she communicated the best way she could that she needed more. John laughed at her, but his eyes were bright and he dutifully pushed her to that edge again before she felt him between her legs.

He coaxed her through it, and while it took a few moments for her body to adjust to his girth, the whole time he kissed her and bit at her ear and neck, using one hand to support himself as the other fondled her breasts. Soon enough he started moving in and out and his fingers slid down to coax a reaction from the same spot as before. Her legs automatically pushed up, providing him with more room, cradling him and they were both panting by the time she felt her body tighten and shudder through the vibrations of completion again and this time John went still above her. She felt his length pulse inside her and he let out a low moan as his thrusts slowed and became smaller, finally stilling.

He pulled out and threw the protection he had used away before wrapping himself around her, kissing her shoulder.

“This is weird, you know,” he said with a little huff of laughter.

Atlantis turned into him and laid a hand on his cheek, just touching their lips together. “I know.”

~~~

In the weeks after, Atlantis came to know each of John’s team as a human and not just as a city. She portrayed herself as a scholar—a master of history, John called her—who had traveled from world to world learning and studying things. 

Weir was always willing and eager, in her calm way, to sit and talk about what Atlantis felt she could share about the Ancients, without giving herself away. If there was no pressing business—rare, but it happened—she and Weir would sit for hours and Atlantis imagined herself as a good friend to the creator-like woman.

Teyla was an entirely different person, both because she was a foreigner without the gene and because Atlantis’ background sensors could feel the Wraith gene that she had. She had felt Teyla’s nightmares long ago and knew she was no threat, but it was awkward at the beginning until she beat Teyla in stick fighting one day. It seemed what was weapons knowledge city-wise, became physical fighting skills in the human body. After that, all fear of Teyla ceased and they too became good friends.

Atlantis often was found by John in the science labs. John was always highly amused by her and McKay’s interaction as the man clearly refused to acknowledge that “Lantia” could do anything as well as he could with Ancient technology, and yet grudgingly respected her at the same time. She couldn’t help but notice though, that he would not open up to her the way everyone else did and this both hurt her and made her feel smug.

Not understanding, she asked John about why her human mind felt so conflicted.

He laughed and suddenly she felt angered. Seeing her expression, John immediately stopped and reached to pull her into an embrace.

“Oh, Atlantis, I didn’t mean to laugh at you.” He kissed her forehead then looked sedately at her. “Do you remember when you first appeared like this, that night?

She nodded.

“I said McKay was jealous. Remember that?”

Recalling, she again nodded.

“That’s what you’re feeling. You’re jealous.”

It took her a moment to consider, but then it hit her. She was jealous. It had happened that first night, too, when John had talked to McKay without her. She felt ashamed.

“Oh, John, what am I going to do? It’s clear I can’t be with you forever like this, and--”

“Wait, you can’t?” John’s eyes went wide, searching her face, hands possessive on her shoulders.

She looked up at him, knowing in that moment, that she couldn’t. Not for the reasons he thought. She could stay in this matter form, this body, for as long as it lived. But one day soon, the city would need her full attention. One day…John would not want her.

She had always known it, known she didn’t feel the empty place inside him heal just because she was human. He wanted—needed—companionship; needed her, even. But it wasn’t enough. And if she wanted him whole, wanted him, she would need to find what would fix him and become the city again.

But, understanding how fragile human emotions were, now that she felt them too, she just responded with, “Yes, I can. I’m sorry, John. Don’t worry.”

He relaxed against her, holding her tight, and she took the relief and made it her own, knowing that soon it wouldn’t be the same. 

That night, their sex was bittersweet.

~~~

It happened sooner than she expected.

The very next week, a mission went bad and she couldn’t help her human gut clenching in terror at the thought that John might be injured. She and Weir waited at the top of the stairs, listening to the yelling and the blasts in the background as John called for a medical team to be ready on spot the moment they came through the gate.

Both watched stricken, albeit for different reasons, as his team came back through. Atlantis noted that though John had streaks of blood on him, he was walking fine, and her background sensors picked up nothing unstable about his health beyond being out of breath with high levels of adrenaline. She could feel his fear, worry, anger, though and it didn’t sit well with her as Teyla and Lorne came through the gate, also unharmed.

Then, she understood as a silent Ronan carried McKay through in his arms and all of her sensors went crazy. The doctor was right there, gurney on hand and John didn’t even look up, though he knew she always watched with Weir. 

“Hey, buddy, it’s going to be okay,” he said as McKay groaned, staying glued to the scientist’s side as he was wheeled to the infirmary.

Weir turned to her and her eyes were sad as she laid a hand on Atlantis’ arm before going down to get a report from Lorne.

She knew this was it. It was time to let him go. If only he saw and understood, it would be right.

Several hours later she went down to the infirmary, finding John pacing back and forth in front of a sleepy and grumbling McKay.

“Sit down, Sheppard, would you? You’re making me dizzy and I don’t need that right—” He cut off as Atlantis walked into the room.

“Hello.”

“Hey, Lantia. Sorry I haven’t been up to—”

She laid her fingers over his mouth. “Shh, John. McKay wants quiet, remember?” She smiled.

“See, even Lantia knows I shouldn’t be disturbed.”

John rolled his eyes and she felt a little flutter but pushed it down to focus. “John, can I talk to McKay alone?”

“Alone, huh?” John raised his eyebrow, but she pushed him out of the room, keeping her expression clear and happy. 

“It won’t take long. Go change. You stink.”

He grinned and waggled his eyebrows at her before leaning down to give her a kiss. She kissed back, her hand creeping up to rest on his chest for a moment before pushing him away again.

“Go.”

She watched him leave before turning back to McKay. He was refusing to look at her, sullenly staring at the wall. When she refused to speak, instead playing with a curl that had fallen from her updo, he finally heaved a big sigh and turned to look at her.

“What do you want?” he snapped.

She walked over to his bed, crossing her arms and steeling herself. McKay could be intimidating when he wanted to be. Even to a city.

“You know he’s in love with you, right?”

McKay’s mouth dropped, and she couldn’t help the twinge of satisfaction at the expression. 

Getting himself under control, he spluttered out, “Excuse me? What right do you have to say…how do you think you know his feelings…not to mention it’s none of your business! What, you think you can just taunt me, before you, I don’t know, kill me or something?” He looked at her suspiciously and inched away. “That’s what you’re here to do, aren’t you? Going to finish the job the wraith started today? You just can’t stand to have me around because he pays attention to me sometimes and not you--”

She covered his mouth with her hand, making a face when he kept talking and he finally shut up.

“Don’t you get it? I _know_ he’s in love with you. And clearly, you’re taken with him, too. But you’re too oblivious or stupid to do something about it.”

“I’m the smartest scientist in two galaxies, I don’t think you have the right to call me stu--”

“Then don’t be!” The lights flickered, the city feeling her ire and frustration.

McKay stared at her. She’d never once raised her voice in the weeks she’d been human, knowing if she did, the energy systems would reflect it, fluctuating.

“If,” she continued, “you insist you are not too stupid to just not have done something about it, then I’ll assume it was ignorance. Having informed you, I expect you will follow through with action.”

She kept her face stern as McKay gaped. She started to walk towards the door, when his voice stopped her.

“What about you? You’re all he thinks about, he’s with you twenty-four seven, he certainly acts like he’s in love with you, not me.”

She turned back to him, sitting herself in the chair next to his bed.

“He loves me, sure. He loves what I offer him, and don’t look at me that way. I did not mean it in a sexual manner.” She took a breath, smoothing her hands over the wrinkles in her grey pants. “I offered him what he thought he wanted. But there’s a lot about John you don’t know, and a lot I’m only now coming to understand in actuality. I’ve given him all I can.

“There’s a huge hole in him, Doctor. And I’ve tried to fix it, but it doesn’t need me. From what I’ve seen, what I know of John…you’re the only thing that can make him whole again. You two balance each other out, and not just brawn and brains, because if you can’t see he’s smart too, you don’t deserve him.”

She clenched her hands in the fabric on her thighs. 

“You know now, so do something about it. He was scared that you were going to die today. He’s not scared of that for me. He knows I’ll be alright. And I can depend on him. But it’s not the same. We can’t ever be like you and he can be. We’re too…different.

“So, I’m going to leave. You won’t be able to find me again, not like this. But I swear, if you break his heart…I have ways. I will make sure you atone.”

She glanced up at the man in the bed, noticed he was looking a little pale and handed him a cup of water from beside the bed. He took it and gulped greedily. He came up for air, setting it back on the little table. If she focused, she could feel the tiny tremors running through his body with her sensors.

“I know.”

“Know what?” she questioned, confused.

“I know that he’s smart. Did you think I only like him because he has great hair? The man’s a math whiz, he’s a genius at tactical operations, he lives and loves life, and he’s saved mine more than I could ever count. He’s got this passion…” 

He trailed off, looking down at his hands, mouth twisting like it always did when he was upset but trying not to show it.

“You really think…you think he loves me? Me, Rodney McKay. Brilliant scientist, yes, but one with no social skills, I’m a jerk, oh, and there’s the fact that I certainly don’t look like you.”

She smiled softly. “I know he does. He might not know it himself, but I think if you gave something of yourself…it’ll come to him.”

They were silent for some time, both entertaining thoughts about John. Then she felt a build-up in her throat and it was hard to swallow, hard to breathe.

“McKay, how can I do this? I don’t know how to give him up.” A noise tore from her throat and she was startled and confused, unsure what was happening to her.

“Er, there, there,” McKay said, patting her arm awkwardly. “Don’t cry, I—”

Whatever else he said was lost to her. Cry. That’s what she was doing. And she noticed the lights slowly fading, turning the city dark as she felt the tears drain away her anger and sorrow.

She allowed herself a minute more before she picked her head up from her arms resting on McKay’s bed. The lights gained strength again as she did.

“I am sorry, Doctor. Forgive me, please, for my lapse.”

“It’s, ah, no problem.”

She nodded, wiping the water from her face. She stood up to go and leaned down at the last moment to give McKay a kiss on the forehead.

“Treat him well. He deserves that and so much more.”

McKay shifted, obviously uncomfortable, but then he jerked his head, his own version of an accepting nod.

As she passed through the door, he called out.

“Lantia! The lights…you were angry, crying…your name…”

She looked back with an all-knowing, “Mona Lisa” smile, as John called it, then left.

After all, Rodney McKay was the smartest scientist in two galaxies.

~~~

Three days later, she was gone and after John had searched in vain for her, he finally understood, and informed the team that “Lantia” had had to return to care for her people and that they would not be seeing her again. The whole expedition radiated sadness and Atlantis found herself overwhelmed with gratefulness and protectiveness towards them. 

She had kept silent since she’d let the body fade, unable to deal with her own grief and John’s at the same time. She kept everything on autopilot and sunk into herself, wondering if she’d lost everything.

By the end of the second night, John was screaming at her in his head, asking her why she left, how she thought he could be without her. Asking her why, when he was the damn military man, she had to go off and try to be a hero by saving him from whatever she thought he needed to be saved from.

But on the third night, hours after he told the crew of the her city that the woman he’d been with for weeks wouldn’t be around anymore, she noted McKay walking slowly and skittishly to John’s room.

When he got there, he was muttering to himself, pacing in front of the door, and she roused herself, bringing her main consciousness to the forefront once again. He leaned against the wall, and she sent a calming thought through it, knowing the contact would help him understand a little more.

_*It’s ok. Go.*_

He started as though he could actually hear her and turned to the door.

She opened it just as he was about to knock.

John looked up from polishing his weapon.

“McKay, what--?”

The other man stepped into the room and she followed the tread of his feet to the bed and she knew from the shock and amazement that echoed in John’s mind that McKay was kissing him.

“Oh,” she heard John say, and felt his amazement grow. “You…”

“Sheppard.”

And just then, she felt that hole inside John begin to heal. Not much, and not fast. But she knew that this, this is what it was he needed to be whole, and that in time, he would become whole again.

_Thank you. But what about--_

_*You are my king.*_

_I’ll miss you._

_*No, you won’t. I am always here.*_

**Author's Note:**

> Follow and chat with me [on tumblr](http://mf-luder-xf.tumblr.com)!


End file.
